removeLowQualitySamples {beadarraySNP} | R Documentation

## Quality control of SnpSetIllumina objects

### Description

Remove samples from a SnpSetIllumina object that show a low quality

### Usage

    removeLowQualitySamples(object, min.intensity = 1500, min.gt = 100, subsample = "OPA")

### Arguments

`object` | `SnpSetIllumina-class` object
`min.intensity` | `numeric`. Samples that show a median intensity below this value in either Red or Green channel are removed
`min.gt` | `numeric`. Samples that have less than this amount of valid genotypes are removed
`subsample` | factor or column name in `featureData` slot of `object`

### Value

This function returns an `SnpSetIllumina` object.

### Author(s)

Jan Oosting

### Examples

      data(chr17.260)
      chr17.260<-removeLowQualitySamples(chr17.260,min.gt=10)

[Package beadarraySNP version 1.60.0 Index]